533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/genoLay.c src/hg/cgilib/genoLay.c
new file mode 100644
index 0000000..417d7b4
--- /dev/null
+++ src/hg/cgilib/genoLay.c
@@ -0,0 +1,564 @@
+/* genoLay - genome layout. Arranges chromosomes so that they
+ * tend to fit together nicely on a single page. */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
+#include "common.h"
+#include "hash.h"
+#include "jksql.h"
+#include "vGfx.h"
+#include "cytoBand.h"
+#include "hCytoBand.h"
+#include "genoLay.h"
+
+
+void genoLayDump(struct genoLay *gl)
+/* Print out info on genoLay */
+{
+struct genoLayChrom *chrom;
+struct slRef *left, *right, *ref;
+int total;
+printf("gl: lineCount %d, leftLabelWidth %d, rightLabelWidth %d, basesPerPixel %f<BR>\n",
+	gl->lineCount, gl->leftLabelWidth, gl->rightLabelWidth, gl->basesPerPixel);
+for (left = gl->leftList, right = gl->rightList; left != NULL || right != NULL;)
+    {
+    total=0;
+    if (left != NULL)
+	{
+	chrom = left->val;
+	printf("%s@%d,%d[%d] %d ----  ", chrom->fullName, chrom->x, chrom->y, chrom->width, chrom->size);
+	total += chrom->size;
+        left = left->next;
+	}
+    if (right != NULL)
+	{
+	chrom = right->val;
+	printf("%d  %s@%d,%d[%d]", chrom->size, chrom->fullName, chrom->x, chrom->y, chrom->width);
+	total += chrom->size;
+        right = right->next;
+	}
+    printf(" : %d<BR>", total);
+    }
+total=0;
+for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+    {
+    chrom = ref->val;
+    total += chrom->size;
+    printf("%s@%d,%d[%d] %d ...  ", chrom->fullName, chrom->x, chrom->y, chrom->width, chrom->size);
+    }
+printf(" : %d<BR>", total);
+}
+
+int genoLayChromCmpName(const void *va, const void *vb)
+/* Compare two chromosome names so as to sort numerical part
+ * by number.. */
+{
+const struct genoLayChrom *a = *((struct genoLayChrom **)va);
+const struct genoLayChrom *b = *((struct genoLayChrom **)vb);
+char *aName = a->shortName, *bName = b->shortName;
+if (isdigit(aName[0]))
+    {
+    if (isdigit(bName[0]))
+	{
+	int diff = atoi(aName) - atoi(bName);
+	if (diff == 0)
+	    diff = strcmp(skipNumeric(aName), skipNumeric(bName));
+	return diff;
+	}
+    else
+        return -1;
+    }
+else if (isdigit(bName[0]))
+    return 1;
+else
+    return strcmp(aName, bName);
+}
+
+struct genoLayChrom *genoLayDbChromsExt(struct sqlConnection *conn, 
+	boolean withRandom, boolean abortOnErr)
+/* Get chrom info list. */
+{
+struct sqlResult *sr;
+char **row;
+struct genoLayChrom *chrom, *chromList = NULL;
+sr = sqlGetResult(conn, NOSQLINJ "select chrom,size from chromInfo");
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    char *name = row[0];
+    if (withRandom || 
+        (
+        (startsWith("chr", name))
+     && (!startsWith("chrUn", name))
+     && (!sameString("chrM", name))
+     && (!strchr(name, '_'))   // avoiding _random and _hap*
+	)
+       )
+	{
+	AllocVar(chrom);
+	chrom->fullName = cloneString(name);
+	chrom->shortName = chrom->fullName+3;
+	chrom->size = sqlUnsigned(row[1]);
+	slAddHead(&chromList, chrom);
+	}
+    }
+if (chromList == NULL)
+    {
+    if (abortOnErr)
+    	errAbort("No chromosomes found in chromInfo.");
+    return NULL;
+    }
+int count = slCount(chromList);
+if (count > 500)
+    {
+    if (abortOnErr)
+	errAbort("Sorry, cannot do genome layout on an assembly "
+    	    "with too many (%d) chromosomes exceeds 500. "
+    	    "Please select another organism or assembly.", count);
+    }
+slReverse(&chromList);
+slSort(&chromList, genoLayChromCmpName);
+return chromList;
+}
+
+struct genoLayChrom *genoLayDbChroms(struct sqlConnection *conn, 
+	boolean withRandom)
+/* Get chrom info list. */
+{
+return genoLayDbChromsExt(conn, withRandom, TRUE);
+}
+
+
+static void separateSexChroms(struct slRef *in,
+	struct slRef **retAutoList, struct slRef **retSexList)
+/* Separate input chromosome list into sex and non-sex chromosomes. */
+{
+struct slRef *autoList = NULL, *sexList = NULL, *ref, *next;
+
+for (ref = in; ref != NULL; ref = next)
+    {
+    struct genoLayChrom *chrom = ref->val;
+    char *name = chrom->shortName;
+    next = ref->next;
+    if (sameWord(name, "X") || sameWord(name, "Y") || sameWord(name, "Z")
+    	|| sameWord(name, "W"))
+	{
+	slAddHead(&sexList, ref);
+	}
+    else
+        {
+	slAddHead(&autoList, ref);
+	}
+    }
+slReverse(&sexList);
+slReverse(&autoList);
+*retAutoList = autoList;
+*retSexList = sexList;
+}
+
+struct genoLay *genoLayNew(struct genoLayChrom *chromList,
+	MgFont *font, int picWidth, int betweenChromHeight,
+	int minLeftLabelWidth, int minRightLabelWidth,
+	char *how)
+/* Figure out layout.  For human and most mammals this will be
+ * two columns with sex chromosomes on bottom.  This is complicated
+ * by the platypus having a bunch of sex chromosomes. */
+{
+int margin = 3;
+struct slRef *refList = NULL, *ref, *left, *right;
+struct genoLayChrom *chrom;
+struct genoLay *gl;
+int autoCount, halfCount, bases;
+int leftLabelWidth=0, rightLabelWidth=0, labelWidth;
+int spaceWidth = mgFontCharWidth(font, ' ');
+int extraLabelPadding = 0;
+int autosomeOtherPixels=0, sexOtherPixels=0;
+int autosomeBasesInLine=0;	/* Maximum bases in a line for autosome. */
+int sexBasesInLine=0;		/* Bases in line for sex chromsome. */
+double sexBasesPerPixel, autosomeBasesPerPixel, basesPerPixel;
+int pos = margin;
+int y = 0;
+int fontHeight = mgFontLineHeight(font);
+int chromHeight = fontHeight;
+int lineHeight = chromHeight + betweenChromHeight;
+boolean allOneLine = FALSE;
+
+refList = refListFromSlList(chromList);
+
+/* Allocate genoLay object and fill in simple fields. */
+AllocVar(gl);
+gl->chromList = chromList;
+gl->chromHash = hashNew(0);
+gl->font = font;
+gl->picWidth = picWidth;
+gl->margin = margin;
+gl->spaceWidth = spaceWidth;
+gl->lineHeight = lineHeight;
+gl->betweenChromHeight = betweenChromHeight;
+gl->betweenChromOffsetY = 0;
+gl->chromHeight = chromHeight;
+gl->chromOffsetY = lineHeight - chromHeight;
+
+
+/* Save chromosomes in hash too, for easy access */
+for (chrom = chromList; chrom != NULL; chrom = chrom->next)
+    hashAdd(gl->chromHash, chrom->fullName, chrom);
+
+if (sameString(how, genoLayOnePerLine))
+    {
+    gl->leftList = refList;
+    }
+else if (sameString(how, genoLayAllOneLine))
+    {
+    gl->bottomList = refList;
+    allOneLine = TRUE;
+    }
+else
+    {
+    /* Put sex chromosomes on bottom, and rest on left. */
+    separateSexChroms(refList, &refList, &gl->bottomList);
+    autoCount = slCount(refList);
+    gl->leftList = refList;
+
+    /* If there are a lot of chromosomes, then move later
+     * (and smaller) chromosomes to a new right column */
+    if (autoCount > 12)
+	{
+	halfCount = (autoCount+1)/2;
+	ref = slElementFromIx(refList, halfCount-1);
+	gl->rightList = ref->next;
+	ref->next = NULL;
+	slReverse(&gl->rightList);
+	}
+    }
+
+if (allOneLine)
+    {
+    unsigned long totalBases = 0, bStart=0, bEnd;
+    int chromCount = 0, chromIx=0;
+    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+        {
+	chrom = ref->val;
+	totalBases += chrom->size;
+	chromCount += 1;
+	}
+    int availablePixels = picWidth - minLeftLabelWidth - minRightLabelWidth
+       - 2*margin - (chromCount-1);
+    double basesPerPixel = (double)totalBases/availablePixels;
+    gl->picHeight = 2*margin + lineHeight + fontHeight;
+    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+        {
+	chrom = ref->val;
+	bEnd = bStart + chrom->size;
+	int pixStart = round(bStart / basesPerPixel);
+	int pixEnd = round(bEnd / basesPerPixel);
+	chrom->width = pixEnd - pixStart;
+	chrom->height = lineHeight;
+	chrom->x = pixStart + margin + chromIx + minLeftLabelWidth;
+	chrom->y = 0;
+	chromIx += 1;
+	bStart = bEnd;
+	}
+    gl->lineCount = 1;
+    gl->picHeight = 2*margin + lineHeight + fontHeight + 1;
+    gl->allOneLine = TRUE;
+    gl->leftLabelWidth = minLeftLabelWidth;
+    gl->rightLabelWidth = minRightLabelWidth;
+    gl->basesPerPixel = basesPerPixel;
+    gl->pixelsPerBase = 1.0/basesPerPixel;
+    }
+else
+    {
+    /* Figure out space needed for autosomes. */
+    left = gl->leftList;
+    right = gl->rightList;
+    while (left || right)
+	{
+	bases = 0;
+	if (left)
+	    {
+	    chrom = left->val;
+	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
+	    if (leftLabelWidth < labelWidth)
+		leftLabelWidth = labelWidth;
+	    bases = chrom->size;
+	    left = left->next;
+	    }
+	if (right)
+	    {
+	    chrom = right->val;
+	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
+	    if (rightLabelWidth < labelWidth)
+		rightLabelWidth = labelWidth;
+	    bases += chrom->size;
+	    right = right->next;
+	    }
+	if (autosomeBasesInLine < bases)
+	    autosomeBasesInLine = bases;
+	gl->lineCount += 1;
+	}
+
+    /* Figure out space needed for bottom chromosomes. */
+    if (gl->bottomList)
+	{
+	gl->lineCount += 1;
+	sexOtherPixels = spaceWidth + 2*margin;
+	for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+	    {
+	    chrom = ref->val;
+	    sexBasesInLine += chrom->size;
+	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
+	    if (ref == gl->bottomList )
+		{
+		if (leftLabelWidth < labelWidth)
+		    leftLabelWidth  = labelWidth;
+		sexOtherPixels = leftLabelWidth;
+		}
+	    else if (ref->next == NULL)
+		{
+		if (rightLabelWidth < labelWidth)
+		    rightLabelWidth  = labelWidth;
+		sexOtherPixels += rightLabelWidth + spaceWidth;
+		}
+	    else
+		{
+		sexOtherPixels += labelWidth + spaceWidth;
+		}
+	    }
+	}
+
+    /* Do some adjustments if side labels are bigger than needed for
+     * chromosome names. */
+    if (leftLabelWidth < minLeftLabelWidth)
+	{
+	extraLabelPadding += (minLeftLabelWidth - leftLabelWidth);
+	leftLabelWidth = minLeftLabelWidth;
+	}
+    if (rightLabelWidth < minRightLabelWidth)
+	{
+	extraLabelPadding += (minRightLabelWidth - rightLabelWidth);
+	rightLabelWidth = minRightLabelWidth;
+	}
+    sexOtherPixels += extraLabelPadding;
+
+    /* Figure out the number of bases needed per pixel. */
+    autosomeOtherPixels = 2*margin + spaceWidth + leftLabelWidth + rightLabelWidth;
+    basesPerPixel = autosomeBasesPerPixel 
+	    = autosomeBasesInLine/(picWidth-autosomeOtherPixels);
+    if (gl->bottomList)
+	{
+	sexBasesPerPixel = sexBasesInLine/(picWidth-sexOtherPixels);
+	if (sexBasesPerPixel > basesPerPixel)
+	    basesPerPixel = sexBasesPerPixel;
+	}
+
+    /* Save positions and sizes of some things in layout structure. */
+    gl->leftLabelWidth = leftLabelWidth;
+    gl->rightLabelWidth = rightLabelWidth;
+    gl->basesPerPixel = basesPerPixel;
+    gl->pixelsPerBase = 1.0/basesPerPixel;
+
+    /* Set pixel positions for left autosomes */
+    for (ref = gl->leftList; ref != NULL; ref = ref->next)
+	{
+	chrom = ref->val;
+	chrom->x = leftLabelWidth + margin;
+	chrom->y = y;
+	chrom->width = round(chrom->size/basesPerPixel);
+	chrom->height = lineHeight;
+	y += lineHeight;
+	}
+
+    /* Set pixel positions for right autosomes */
+    y = 0;
+    for (ref = gl->rightList; ref != NULL; ref = ref->next)
+	{
+	chrom = ref->val;
+	chrom->width = round(chrom->size/basesPerPixel);
+	chrom->height = lineHeight;
+	chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
+	chrom->y = y;
+	y += lineHeight;
+	}
+    gl->picHeight = 2*margin + lineHeight * gl->lineCount;
+    y = gl->picHeight - margin - lineHeight;
+
+    /* Set pixel positions for sex chromosomes */
+    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+	{
+	chrom = ref->val;
+	chrom->y = y;
+	chrom->width = round(chrom->size/basesPerPixel);
+	chrom->height = lineHeight;
+	if (ref == gl->bottomList)
+	    chrom->x = leftLabelWidth + margin;
+	else if (ref->next == NULL)
+	    chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
+	else
+	    chrom->x = 2*spaceWidth+mgFontStringWidth(font,chrom->shortName) + pos;
+	pos = chrom->x + chrom->width;
+	}
+    }
+return gl;
+}
+
+static void leftLabel(struct hvGfx *hvg, struct genoLay *gl,
+	struct genoLayChrom *chrom, int yOffset, int fontHeight,
+	int color)
+/* Draw a chromosome with label on left. */
+{
+hvGfxTextRight(hvg, gl->margin, chrom->y + yOffset, 
+    chrom->x - gl->margin - gl->spaceWidth, fontHeight, color,
+    gl->font, chrom->shortName);
+}
+
+static void rightLabel(struct hvGfx *hvg, struct genoLay *gl,
+	struct genoLayChrom *chrom, int yOffset, int fontHeight, 
+	int color)
+/* Draw a chromosome with label on left. */
+{
+hvGfxText(hvg, chrom->x + chrom->width + gl->spaceWidth,
+	chrom->y + yOffset, 
+	color, gl->font, chrom->shortName);
+}
+
+static void midLabel(struct hvGfx *hvg, struct genoLay *gl,
+	struct genoLayChrom *chrom, int yOffset, int fontHeight, 
+	int color)
+/* Draw a chromosome with label on left. */
+{
+MgFont *font = gl->font;
+int textWidth = mgFontStringWidth(font, chrom->shortName);
+hvGfxTextRight(hvg, chrom->x - textWidth - gl->spaceWidth, 
+    chrom->y + yOffset, 
+    textWidth, fontHeight, color,
+    font, chrom->shortName);
+}
+
+void genoLayDrawChromLabels(struct genoLay *gl, struct hvGfx *hvg, int color)
+/* Draw chromosomes labels in image */
+{
+struct slRef *ref;
+struct genoLayChrom *chrom;
+int pixelHeight = mgFontPixelHeight(gl->font);
+if (gl->allOneLine)
+    {
+    int yOffset = gl->chromOffsetY + gl->chromHeight + 1;
+
+    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+	{
+	chrom = ref->val;
+	hvGfxTextCentered(hvg, chrom->x, yOffset, chrom->width, pixelHeight, color, gl->font,
+		chrom->shortName);
+	}
+    }
+else
+    {
+    int yOffset = gl->chromOffsetY + gl->chromHeight - pixelHeight;
+
+    /* Draw chromosome labels. */
+    for (ref = gl->leftList; ref != NULL; ref = ref->next)
+	leftLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
+    for (ref = gl->rightList; ref != NULL; ref = ref->next)
+	rightLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
+    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
+	{
+	chrom = ref->val;
+	if (ref == gl->bottomList)
+	    leftLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
+	else if (ref->next == NULL)
+	    rightLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
+	else
+	    midLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
+	}
+    }
+}
+
+void genoLayDrawSimpleChroms(struct genoLay *gl,
+	struct hvGfx *hvg, int color)
+/* Draw boxes for all chromosomes in given color */
+{
+int height = gl->chromHeight;
+int yOffset = gl->chromOffsetY;
+struct genoLayChrom *chrom;
+for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
+    hvGfxBox(hvg, chrom->x, chrom->y + yOffset, 
+	chrom->width, height, color);
+
+}
+
+void genoLayDrawBandedChroms(struct genoLay *gl, struct hvGfx *hvg, char *db,
+	struct sqlConnection *conn, Color *shadesOfGray, int maxShade, 
+	int defaultColor)
+/* Draw chromosomes with centromere and band glyphs. 
+ * Get the band data from the database.  If the data isn't
+ * there then draw simple chroms in default color instead */
+{
+char *bandTable = "cytoBandIdeo";
+int yOffset = gl->chromOffsetY;
+genoLayDrawSimpleChroms(gl, hvg, defaultColor);
+if (sqlTableExists(conn, bandTable) && !gl->allOneLine)
+    {
+    int centromereColor = hCytoBandCentromereColor(hvg);
+    double pixelsPerBase = 1.0/gl->basesPerPixel;
+    int height = gl->chromHeight;
+    int innerHeight = gl->chromHeight-2;
+    struct genoLayChrom *chrom;
+    boolean isDmel = hCytoBandDbIsDmel(db);
+    boolean bColor = hvGfxFindColorIx(hvg, 200, 150, 150);
+    int fontPixelHeight = mgFontPixelHeight(gl->font);
+    for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
+	{
+	struct sqlResult *sr;
+	char **row;
+	char query[256];
+	int cenX1=BIGNUM, cenX2=0;
+	int y = chrom->y + yOffset;
+
+	/* Fetch bands from database and draw them. */
+	sqlSafef(query, sizeof(query), "select * from %s where chrom='%s'",
+		bandTable, chrom->fullName);
+	sr = sqlGetResult(conn, query);
+	while ((row = sqlNextRow(sr)) != NULL)
+	    {
+	    struct cytoBand band;
+	    int x1, x2;
+	    cytoBandStaticLoad(row, &band);
+	    x1 = pixelsPerBase*band.chromStart;
+	    x2 = pixelsPerBase*band.chromEnd;
+	    if (sameString(band.gieStain, "acen"))
+		{
+		/* Centromere is represented as two adjacent bands.
+		 * We'll just record the extents of it here, and draw it
+		 * in one piece later. */
+		if (x1 < cenX1)
+		    cenX1 = x1;
+		if (x2 > cenX2)
+		    cenX2 = x2;
+		}
+	    else
+		{
+		/* Draw band */
+		hCytoBandDrawAt(&band, hvg, x1+chrom->x, y+1, x2-x1, innerHeight, 
+			isDmel, gl->font, fontPixelHeight, MG_BLACK, bColor,
+		    shadesOfGray, maxShade);
+		}
+	    }
+	sqlFreeResult(&sr);
+
+	/* Draw box around chromosome */
+	hvGfxBox(hvg, chrom->x, y, chrom->width, 1, MG_BLACK);
+	hvGfxBox(hvg, chrom->x, y+height-1, chrom->width, 1, MG_BLACK);
+	hvGfxBox(hvg, chrom->x, y, 1, height, MG_BLACK);
+	hvGfxBox(hvg, chrom->x+chrom->width-1, y, 1, height, MG_BLACK);
+
+	/* Draw centromere if we found one. */
+	if (cenX2 > cenX1)
+	    {
+	    hCytoBandDrawCentromere(hvg, cenX1+chrom->x, y, cenX2-cenX1, height,
+	       MG_WHITE, centromereColor);
+	    }
+	}
+    }
+}
+